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Decoding PRC2 stage-specific roles during germline-embryo-germline transition

GSE298615 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 62 samples Submitted 2026/03/11 Platform GPL32159
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 62 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
62 samples: 31 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Decoding the cell intrinsic and extrinsic roles of PRC2 in early embryogenesisbioRxiv : the preprint server for biology · 2026
Summary (written by the submitters)
Early mammalian development undergoes a series of precisely regulated processes, including the maternal-to-zygotic transition (MZT), the first lineage specifications, gastrulation, and the primordial germ cell (PGC) specification. While key transcription factors (TFs) and epigenetic modifiers that regulate these events have been investigated, the intricate transcriptional and epigenetic networks, such as interplays between TFs and chromatin modifications remain to be fully established.
Read the full summary ↓
The Polycomb Repressive Complex 2 (PRC2) mediates transcriptional silencing by depositing H3K27me3 and is essential for proper gastrulation. However, the PRC2 function in early development may not be fully captured due to limitations of conventional knockout approaches. Here we applied the degradation tag (dTAG) system to deplete the PRC2 acutely and stage-specifically in mouse pre- and early post-implantation development. This work revealed previously underappreciated functions of PRC2 in regulating key events in early development including the MZT, the first and second cell lineage specifications. In addition, we demonstrated that PRC2 restricts premature activation of developmental genes in embryonic day (E)4.5 inner cell mass (ICM) cells, facilitating proper epiblast specification. Moreover, systematic analysis of H3K27me3 and H3K4me3 dynamics reveals that epigenetics interplay drives the chromatin bivalency establishment at E4.5 ICM, which is earlier than previously thought that the bivalency appears at post-implantation stages. Lastly, we elucidated the lineage crosstalk dependent PRC2-ESRRB-BMP4 signal axis in regulating PGCs specification during gastrulation. Together, our results demonstrate that PRC2 plays stage-specific roles through dual interplay with epigenetic modification and transcription factors during germline-embryo-germline transition.
Published in
Decoding the cell intrinsic and extrinsic roles of PRC2 in early embryogenesis
Zhou C, Wang M, Chen Z et al. · bioRxiv : the preprint server for biology 2026 · PMID 41648125 · doi:10.64898/2026.01.20.700679
This dataset
Open GSE298615 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE298615_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1270026 and SRA study SRP588896. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41648125) ↗
Study design
31 conditions, mostly in duplicate
RNA_E2C_EED_DMSO ×2 RNA_E2C_EED_dTAG ×2 RNA_L2C_EED_DMSO ×2 RNA_L2C_EED_dTAG ×2 RNA_Morula_EED_DMSO ×2 RNA_Morula_EED_dTAG ×2 RNA_E4.5_ICM_EED_DMSO ×2 RNA_E4.5_ICM_EED_dTAG ×2 +23 more

Supports a between-group comparison across 62 samples.

How we read this: 31 replicated groups read from 62 sample titles; they account for 62 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 22 more — browse all 62 samples with per-sample file links →

Datasets on a similar topic

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